1SUW

Crystal structure of a NAD kinase from Archaeoglobus fulgidus in complex with its substrate and product: Insights into the catalysis of NAD kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structures of an NAD Kinase from Archaeoglobus fulgidus in Complex with ATP, NAD, or NADP

Liu, J.Lou, Y.Yokota, H.Adams, P.D.Kim, R.Kim, S.-H.

(2005) J.Mol.Biol. 354: 289-303

  • DOI: 10.1016/j.jmb.2005.09.026
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • NAD kinase is a ubiquitous enzyme that catalyzes the phosphorylation of NAD to NADP using ATP or inorganic polyphosphate (poly(P)) as phosphate donor, and is regarded as the only enzyme responsible for the synthesis of NADP. We present here the cryst ...

    NAD kinase is a ubiquitous enzyme that catalyzes the phosphorylation of NAD to NADP using ATP or inorganic polyphosphate (poly(P)) as phosphate donor, and is regarded as the only enzyme responsible for the synthesis of NADP. We present here the crystal structures of an NAD kinase from the archaeal organism Archaeoglobus fulgidus in complex with its phosphate donor ATP at 1.7 A resolution, with its substrate NAD at 3.05 A resolution, and with the product NADP in two different crystal forms at 2.45 A and 2.0 A resolution, respectively. In the ATP bound structure, the AMP portion of the ATP molecule is found to use the same binding site as the nicotinamide ribose portion of NAD/NADP in the NAD/NADP bound structures. A magnesium ion is found to be coordinated to the phosphate tail of ATP as well as to a pyrophosphate group. The conserved GGDG loop forms hydrogen bonds with the pyrophosphate group in the ATP-bound structure and the 2' phosphate group of the NADP in the NADP-bound structures. A possible phosphate transfer mechanism is proposed on the basis of the structures presented.


    Organizational Affiliation

    Berkeley Structural Genomics Center, Lawrence Berkeley National Laboratory, Physical Bioscience Division, Berkeley, CA 94720-5230, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable inorganic polyphosphate/ATP-NAD kinase
A, B, C, D
249Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)Gene Names: nadK
EC: 2.7.1.23
Find proteins for O30297 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Go to UniProtKB:  O30297
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B, C, D
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.211 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 122.141α = 90.00
b = 122.141β = 90.00
c = 198.595γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
HKL-2000data collection
CNSrefinement
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description